cg (version 1.0-2)

varianceGraph.cgOneFactorFit: Equal Variance Graphs assessment of cgOneFactorFit object

Description

Graph residuals of a cgOneFactorFit object to assess equal variance assumption

Usage

## S3 method for class 'cgOneFactorFit':
varianceGraph(fit, trend = NULL, cgtheme = TRUE,
 device = "single", \dots)

Arguments

fit

A fit object of class cgOneFactorFit.

trend

Add a trend line. When set to the default NULL, the addition of a trend line depends on the following: When there is no censored data, a trend will be added with the lowess smoother.

cgtheme

When set to the default TRUE, ensures a trellis device is active with limited color scheme. Namely background, strip.shingle, and strip.background are each set to "white".

device

Can be one of three values: [object Object],[object Object],[object Object]

...

Additional arguments. Two are currently valid: [object Object]

Value

• varianceGraph.cgOneFactorFit returns an invisible NULL. The main purpose is the side effect of graphing to the current device.

concept

• equal variance
• residual diagnostics

Details

The graph plots the square root of the absolute value of the residuals against the fitted value. The square root spacing on the y-axis has tick marks in the fitted scale. The notion of using the squared root of the absolute residuals is attributed to John Tukey. The values are automatically jittered to minimize overlapping points. For censored data, left-censored values are shown as a shallow "V", which is actually just a rotated downward "<" sign.="" similarly,="" right-censored="" values="" are="" shown="" as="" a="" deeper="" "^",="" which="" is="" rotated="" upward="" "="">" sign. For the trend argument, an added trend line when censored data residuals are present needs to be interpreted cautiously. When there are 7 or more groups, a cubic smoothing spline based on VGAM::vgam is fit; otherwise, the group means of the residuals are estimated with an accelerated failure time model and then just connected. If "too many" censored data values are present, the line may be withheld and warnings will be issued, or if forced with line=TRUE, for example, may appear nonsensical. The heading for the graph is taken from the cgOneFactorData object, which prepareCGOneFactorData sets from its analysisname argument. The label for the Y-axis is taken from the cgOneFactorData object, which prepareCGOneFactorData sets from its endptname argument. The number of decimal places printed in the ticks on the Y-axis is taken from the cgOneFactorData object, which prepareCGOneFactorData sets from its digits argument. The minimum and maximum values from the range of the absolute valued residuals are respectively labeled in the bottom and top left corners of the graph region. If group labels along the x-axis seem to overlap in the standard horizontal form, they will be rotated 45 degrees.

Examples

## From running examples of cgOneFactorData objects
data(canine)
canine.data <- prepareCGOneFactorData(canine, format="groupcolumns",
                                      analysisname="Canine",
                                      endptname="Prostate Volume",
                                      endptunits=expression(plain(cm)^3),
                                      digits=1, logscale=TRUE, refgrp="CC")
canine.fit <- fit(canine.data)

varianceGraph(canine.fit)

varianceGraph(canine.fit, model="olsonly")


gmcsfcens.data <- prepareCGOneFactorData(gmcsfcens, format="groupcolumns",
                                         analysisname="cytokine",
                                         endptname="GM-CSF (pg/ml)",
                                         logscale=TRUE,
                                         digits=1)

gmcsfcens.fit <- fit(gmcsfcens.data, type="aft")

varianceGraph(gmcsfcens.fit, trend=TRUE)

varianceGraph(gmcsfcens.fit) ## will yield a warning message why no line
                             ## is graphed

varianceGraph(gmcsfcens.fit, trend=FALSE)